[gmx-users] g_cluster

Kay Gottschalk kay.gottschalk at weizmann.ac.il
Mon Jan 24 11:48:33 CET 2005

Hi there,

does anyone have experience with g_cluster? I think there are some 

I checked the number of structures in each cluster as written in 
cluster.log. In a second step I used -minstruct xxx, with xxx the 
number of structures in the third cluster. Still, g_cluster reports: 4 
clusters found with at least xxx structures. If I understand things 
correctly, only 3 clusters should be found. Or is the clustering 
process different for each run (I use -method gromos). In 
rmsd-cluster.xpm, different clusters are treated as a single cluster 
giving them all the same color. Since the xpm format is not really 
intuitive for me, I can't easily change that.
If I try to read in a pre-calculated (with g_rms -m)  rmsd-matrix with 
the -dm option, I get the following error:

"Reading rms distance matrix *** malloc[149]: error for object 
0x9002c240: Pointer being reallocated was not allocated
Fatal error: realloc for *matrix (1060 bytes, file matio.c, line 432, 
*matrix=0x0x9002c240): Cannot allocate memory"

Some advice on how to correctly use g_cluster would be highly 

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